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- PDB-7vud: Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans -

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Basic information

Entry
Database: PDB / ID: 7vud
TitleCarotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans
ComponentsCarotenoid cleavage dioxygenase 1
KeywordsPLANT PROTEIN / Carotenoid Cleavage Dioxygenase 1 (CCD1) / lycopene / ionone / psi-ionone / pseudo-ionone.
Function / homology: / carotenoid dioxygenase activity / carotene catabolic process / Carotenoid oxygenase / Retinal pigment epithelial membrane protein / chloroplast stroma / metal ion binding / NICKEL (II) ION / carotenoid 9,10-dioxygenase
Function and homology information
Biological speciesOsmanthus fragrans (sweet osmanthus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSharma, D. / Xue, B.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore) Singapore
CitationJournal: To Be Published
Title: Carotenoid Cleavage Dioxygenase 1 from Osmanthus fragrans
Authors: Sharma, D. / Xue, B.
History
DepositionNov 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carotenoid cleavage dioxygenase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5487
Polymers63,3571
Non-polymers2,1916
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-13 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)209.941, 209.941, 209.941
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein Carotenoid cleavage dioxygenase 1


Mass: 63356.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Osmanthus fragrans (sweet osmanthus) / Gene: CCD1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D4QE74
#2: Chemical ChemComp-OXN / OXTOXYNOL-10 / ALPHA-[4-(1,1,3,3-TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXYPOLY(OXY-1,2-ETHANEDIYL) / TRITON X-100


Mass: 646.849 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H62O11 / Comment: detergent*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 6.09 Å3/Da / Density % sol: 79.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1M Tris pH 7.5, 1.5M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 98.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→49.53 Å / Num. obs: 39479 / % possible obs: 100 % / Redundancy: 81 % / CC1/2: 0.996 / Rmerge(I) obs: 0.0148 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.91 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4387 / CC1/2: 0.38

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3npe

3npe


Resolution: 2.8→49.48 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.469 / SU ML: 0.216 / Cross valid method: FREE R-VALUE / ESU R: 0.303 / ESU R Free: 0.251
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2584 1971 5.003 %
Rwork0.2273 37429 -
all0.229 --
obs-39400 99.964 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 59.231 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4261 0 83 18 4362
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134453
X-RAY DIFFRACTIONr_bond_other_d0.0030.0174236
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.6516026
X-RAY DIFFRACTIONr_angle_other_deg1.391.5799782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6345534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3122.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.61515753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9971520
X-RAY DIFFRACTIONr_chiral_restr0.0680.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021003
X-RAY DIFFRACTIONr_nbd_refined0.2060.2805
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2190.24031
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22117
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.22388
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1070.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4660.234
X-RAY DIFFRACTIONr_nbd_other0.4430.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.090.22
X-RAY DIFFRACTIONr_mcbond_it1.9226.1992139
X-RAY DIFFRACTIONr_mcbond_other1.9236.1982138
X-RAY DIFFRACTIONr_mcangle_it3.1819.3042672
X-RAY DIFFRACTIONr_mcangle_other3.1819.3052673
X-RAY DIFFRACTIONr_scbond_it2.3556.4892313
X-RAY DIFFRACTIONr_scbond_other2.346.4742306
X-RAY DIFFRACTIONr_scangle_it3.7959.6383354
X-RAY DIFFRACTIONr_scangle_other3.8279.6143343
X-RAY DIFFRACTIONr_lrange_it5.35270.2634675
X-RAY DIFFRACTIONr_lrange_other5.36270.2564672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.3791350.3472689X-RAY DIFFRACTION100
2.873-2.9520.3641480.3232649X-RAY DIFFRACTION100
2.952-3.0370.3331260.3132591X-RAY DIFFRACTION100
3.037-3.1310.2971410.2892505X-RAY DIFFRACTION100
3.131-3.2340.2721330.272417X-RAY DIFFRACTION100
3.234-3.3470.341360.2492333X-RAY DIFFRACTION100
3.347-3.4730.2651270.2452277X-RAY DIFFRACTION100
3.473-3.6150.2791110.2292209X-RAY DIFFRACTION100
3.615-3.7760.2261210.2132095X-RAY DIFFRACTION100
3.776-3.960.2481020.2032041X-RAY DIFFRACTION100
3.96-4.1740.2521160.1981908X-RAY DIFFRACTION100
4.174-4.4270.211920.1761848X-RAY DIFFRACTION100
4.427-4.7330.202960.1711722X-RAY DIFFRACTION100
4.733-5.1120.206820.1871618X-RAY DIFFRACTION100
5.112-5.5990.279670.2151518X-RAY DIFFRACTION100
5.599-6.260.248550.2491383X-RAY DIFFRACTION100
6.26-7.2270.268600.2571231X-RAY DIFFRACTION100
7.227-8.8490.265550.2081049X-RAY DIFFRACTION100
8.849-12.5030.181400.188842X-RAY DIFFRACTION100
12.503-49.480.353280.336504X-RAY DIFFRACTION97.4359

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